Software Interfaces

Software for analyzing CellProfiler-produced data

Software Description Interface

CellProfiler Logo


In addition to performing image analysis to generate measurements, CellProfiler has built-in tools in the Data Tools menu to generate a few types of plots. CellProfiler output files in MATLAB (.mat) and HDF5 (.h5) can be opened by CellProfiler's data tools.

CellProfiler Analyst

CellProfiler Analyst

CellProfiler Analyst allows analysis, exploration and machine-learning for high-dimensional image-based data. CellProfiler Analyst can be used with data that follows a simple format: One image table with rows of databases produced in CellProfiler using the ExportToDatabase module or data tool.

Accelrys logo


The Component Collections of the Accelrys Enterprise Platform (AEP) allows researchers to build, deploy, analyze and report on complex scientific data types within the Accelrys applications framework and other third-party applications. The Pipeline Pilot Imaging Component Collection provides a component, 'CellProfiler (on Server)', for integration with CellProfiler. The user can run a protocol and send images to be analyzed into CellProfiler as input, and allows for images and analysis data to be retrieved from CellProfiler for downstream data workflows enabled by AEP. Some details on using the component are provided here.

Columbus logo


The Columbus system (Perkin Elmer) is a universal high-volume image data storage and analysis system that brings access to images from a wide range of sources including all major high content screening instruments via the Internet. Using the final building block (Define Results) of a Columbus analysis routine, data can be exported in a format that CellProfiler Analyst can read. Instructions here.

Excel logoExcel


Prism logoPrism


Calc logo Calc

Spreadsheet programs like these are useful for plotting small amounts of data. Excel (Microsoft) is a general business comercial package, whereas Prism (Graphpad) is a commercial program tailored towards research scientists for statistical analyses. Calc (LibreOffice) is open-source software and freely-available. These tools can read comma- or tab-delimited files generated by the CellProfiler ExportToSpreadsheet module or data tool.

DeNovo Software logo

FCS Express Image Cytometry

FCS Express 4 Image Cytometry (De Novo Software) provides population based analytical tools common in flow cytometry. The image cytometry version allows the user to review and analyze multi-parametric data sets and relate results back to the original images.

FCS Express 4 software can import comma-delimited files produced by the CellProfiler ExportToSpreadsheet module or data tool.

Using CellProfiler and FCS Express 4 Image Cytometry: joint webinar with DeNovo Software on using CellProfiler to peform basic image assays and generate data compatible with export into FCS Express.

Gene Pattern logo


GenePattern (Broad Institute) is open source software that gives a broad audience access to a growing repository of sophisticated analytic tools for genomic data, while an API supports computational biologists. CellProfiler can format and export image-based data as a GenePattern GCT file (.gct) through the ExportToSpreadsheet module or data tool.

IN Cell Analyzer logo

IN Cell Analyzer

IN Cell Analyzer automated cell imaging systems yield morphological and molecular data via high content imaging and analysis. The IN Cell Analyzer acquisition software from GE Healthcare generates customizable CSV reports in a format that allows CellProfiler to import images and metadata via the LoadData module.

KNIME logo


KNIME (University of Konstanz) is an open source modular data exploration platform that enables the user to visually create data flows, selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models. KNIME includes a Database Reader node that can access CellProfiler-produced data. [more]



MATLAB (Mathworks) is a high-level language and interactive environment for data analysis and visualization. CellProfiler can produce MATLAB (.mat) output files.

Orbit logo


Orbit Image Analysis is open source software for quantifying large-format images such as whole slide scans of tissue. It can load images from local disk or connect to an Omero image server and can process images on a local computer or on a cluster using Spark. Orbit can be used to specify a region of interest in a very large image (e.g. a whole-slide scan), and can then send tiled sub-regions to CellProfiler for high-throughput processing of individual cells in each tile. All tiles in the valid ROI are processed via CellProfiler, the results are read back into Orbit and can be visualized.

R logo


Python logo


Any analysis or visualization tools that can query a database (such as R or python+pylab) can be used to analyze data that has been deposited into a MySQL database. Databases containing image and/or object data can be produced using the CellProfiler ExportToDatabase module or data tool. CellProfile-R, an R package for CellProfiler database access and analysis, is available. CellProfiler data generated using the ExportToSpreadsheet module can also be loaded directly into R using any csv file loading function. For an example of how to structure and work with loaded data, see the R Notebook and example pipeline provided here. Users can write their own CellProfiler modules in Python by following the instructions here.

Spotfire logo


Spotfire provides a dynamic, collaborative interface that assimilates data from multiple sources— chemical structures, text, numbers, images, chemical properties, biological assays, and more—and empowers you to perform complex analyses and create easy-to-use visual dashboards. Spotfire is able to import data generated by the CellProfiler ExportToSpreadsheet (for small data sets; see tutorial) or ExportToDatabase modules or data tools (for large data sets).

Software Partnerships

CellProfiler has partnered with academic and commercial groups to create a variety of software interfaces. These efforts not only expand the functionality of CellProfiler and CellProfiler Analyst but also leverage the strengths of other packages.

Software Description Interface

Bioformats logo


Bio-Formats is an open source Java library for reading and writing microscopy file formats. It facilitates the exchange of microscopy data by converting proprietary microscopy data into the OME data model standard. CellProfiler is packaged with Bio-Formats and uses it to read/write images from disk, as well as write movies. [more]

Open Microscopy Envireonment (OME) logo

Open Microcopy Environment (OME)

OMERO is an open source application for visualization, management, and analysis of biological image data. It allows the scientists to remotely manage, view, annotate and measure multi-dimensional images from anywhere. The 2.1.0 release of CellProfiler has first-class support for loading images from OMERO. Details can be found by following this link.

openBIS logo


iBrain logo


OpenBIS is a data management framework to track and annotate raw data for screening, proteomics, FACS and deep sequencing data. iBRAIN is a platform for performing image analysis on large datasets automatically. The SyBIT project, part of SystemsX, delivers integrated analysis pipelines that use CellProfiler as a building block. SyBIT has developed automated workflows for data exchange and analysis based on the openBIS database, CellProfiler, and iBRAIN, using cluster infrastructures for data processing. The project continues to tailor these workflows to suit the research needs of several systems biology projects.